


Brainy's fall

by Bl4ckHunter



Category: Arrow (TV 2012), DC's Legends of Tomorrow (TV), Supergirl (TV 2015), The Flash (TV 2014)
Genre: Not a SuperCorp fic, Other
Language: English
Status: Completed
Published: 2020-03-15
Updated: 2020-04-28
Packaged: 2021-02-28 22:34:27
Rating: Teen And Up Audiences
Warnings: Major Character Death
Chapters: 9
Words: 9,977
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/23154898
Author URL: https://archiveofourown.org/users/Bl4ckHunter/pseuds/Bl4ckHunter
Summary: With one of her closest friends going down a dark path, how far will Kara go to save him from himself?
Kudos: 8





	1. Prologue

**Notes for the Chapter:**

> Something that occured to me after re-watching Supergirl Season 4 and Smallville Seasons 7-10. Timeline-wise, this takes place post-Season 3 of Supergirl, with the exception of no Red Daughter being created by Harun-El. As much as I found the Red Daughter arc in Season 4 interesting, it doesn't work for this story.
> 
> Disclaimer: I do not own DC Comics or the CW TV shows Arrow, The Flash, Legends of Tomorrow, Supergirl or any other characters or elements pertaining to the mentioned franchises.

Brainy was in the lab as he turned around to face Lex Luthor. "No. No." He stepped back, shaking his head before firing a beam from his ring, obliterating Lex as he sighed in relief. "Finally. It's over."

"It'll never be over."

Brainy paled as he whirled around to face Lex again as he stepped back in horror. "H-How…" Lex laughed. "I killed you. You can't be here. I swear, if you hurt my friends—"

"You'll do nothing. Because you can do _nothing_." Lex gloated.

"No." Brainy stepped back, shaking his head and holding it. "No! Just leave me alone! Leave my friends alone!"

"With Myriad I will—"

"Never. I'll stop you." Brainy fired some energy blast from his hand but went straight through Lex.

"Brainy, what are you doing?" Alex demanded.

Brainy turned around to face her before turning to Lex again, who laughed. "Poor Alex."

"No!" Brainy glared, pointing at him. "Leave my friends alone!" He whirled on Alex. "Alex, run!"

* * *

_**Stryker's Island** _

"There's no way he could've escaped." The warden said, accompanying Supergirl and J'onn down the corridor, opening Lex's cell as Lex got up, smirking.

"Supergirl. Mr. J'onzz. To what do I owe this visit?" Lex smirked.

Supergirl took a breath. "Mr. Luthor, have you been recently to DEO?"

"No. I assure you, I haven't left this prison in five years." Lex smiled as Supergirl turned to J'onn, who checked Lex's mind.

"He's telling the truth." J'onn said.

"If Lex was here the whole time, then who…"

* * *

_**DEO** _

Brainy glared at Lex. "I swear, if you as much as lay a finger on her—"

"Brainy, stop! Please, stop! There's nobody there, it's just you!" Alex cried out, tears filling her eyes as he turned to her.

Brainy snorted, shaking his head. "No. That's impossible." He turned around only to notice that "Lex" had vanished. "He… he was right here. I saw him. He must have used some device the instant you entered—"

"No." Alex shook her head, staring at her friend in worry. "I've been watching you for a while and the whole time you've been shouting at the air. Stop!"

"No. No, he must have used something to—"

"Brainy, it's gonna be OK, we're gonna figure this out, OK?" Alex said before her comms went off.

" _Alex, is Brainy there?_ " Kara called out.

"Yeah. And there's something wrong with him, he's been talking with Lex…"

" _But he's not really there, is he?_ " J'onn realized as Alex nodded. " _We just checked in with Stryker's Island. Lex hasn't left the prison and there's no way he could've compromised DEO somehow, they've had him on constant surveillance the whole time. I'm not sure what's going on with Brainy but…_ "

"It's all in his mind." Alex realized. "What's happening to him?"

" _I think we have a pretty good idea. Alex, run. Get as far away from him as possible._ " Kara said as Brainy was falling on his knees, sobbing, as if he was having a breakdown.

Alex neared Brainy, holding him by his shoulder. "Brainy. It's gonna be OK. We can help you."

Suddenly, Brainy got up as he stopped sobbing and he turned around to face Alex and as she looked into his eyes, the look he was giving her was chilling, as she immediately realized that there was something very off about him before she realized that she had seen that cold look before as she paled, realizing who was she facing. "Oh, my God… you… no… not you. It can't be…" She shook her head.

"You're in my way." "Brainy" said darkly as Alex breathed out, horrified.

* * *

_**National City** _

Kara and J'onn were flying in the air before she stopped. "Kara. Is everything OK?" J'onn asked.

Kara paled. "Alex." She tapped her comms. "Alex. Alex, are you there?" She then tried to switch channel. "Nia. Alex isn't answering my calls."

* * *

_**DEO** _

"I'm going to check in on…" Nia stopped as she entered the lab and gasped, stepping back in horror as she saw Alex lying on the floor with a glassy look in her eyes. Nia neared Alex, measuring her pulse before she broke down in tears, sobbing as she closed Alex's eyes.

**Notes for the Chapter:**

> So, what do you guys think? Is it good? Is it bad? Should I continue?
> 
> Please review and let me know if you have been enjoying this.
> 
> With regards
> 
> Bl4ckHunter


	2. Infected

**Summary for the Chapter:**

> After an attempt to stop Children of Liberty, Brainy gets infected by an unknown virus.

**Notes for the Chapter:**

> Imagine that Lockwood got caught and arrested later than in 4x08 and the rest with Manchester Black and the Elite will end rather quickly than how it was dragged out and Lex didn't happen and the president of the U.S. isn't Baker, who was in Lex's pocket but Plastino, the president of the U.S. of Earth Prime after the Crisis, since don't get me started on how stupid and lame villain Lockwood was and while I enjoyed the Lex and Red Daughter arc, it just doesn't work for this story.
> 
> Disclaimer: I do not own DC Comics or the CW TV shows Arrow, The Flash, Legends of Tomorrow, Supergirl or any other characters or elements pertaining to the mentioned franchises.

"Alex! Brainy!" Kara called out as she approached one of the agents. "Hey, Hartmann, have you seen agent Dox and Alex?"

"They were in the labs in the middle level, last I saw them." Hartmann said.

They went downstairs and saw Alex dead on the ground with Nia curled to ball in the corner, sobbing as Kara felt her heart shatter. "No…" Kara knelt towards Alex, trying to wake her up, shaking her. "Alex? Alex?" After a few moments, she broke down in tears, sobbing into Alex's chest.

"Nia?" J'onn turned to her as she still stared in shock. "What happened?"

"I couldn't leave her like this…" Nia whispered.

J'onn knelt towards her, hugging her as she sobbed.

* * *

Barry, Cisco, Caitlin, Ralph and Sherloque came from Earth-1 to talk as they were all in the conference room. "Brainy did this?" Barry asked. "Did he…"

"He killed Alex." Kara said lowly.

"He didn't kill Alex!" Nia exploded as she got up. "That wasn't Brainy! It was his goddamned ancestors who did it! They… somehow he got rebooted because of that virus and they took over his body! Brainy would never have hurt her!"

"Nia…" J'onn tried to console her but she ran off, clearly still in shock.

"Brainy would never hurt Alex, not out of his own volition." Kara said.

"We know, Kara." Cisco assured.

"What virus?" Barry asked, confused.

"What exactly happened?" Caitlin asked.

Kara wiped her face, trying to keep her tears at bay. "It was few weeks after Mar Novu."

Colonel Haley cleared her throat. "Supergirl, with all due respect, I advise against divulging DEO's and governmental secrets to strangers…"

"They're not DEO but they're our allies, Colonel. We trust them." J'onn said and Colonel Haley sighed.

"Very well. If you vouch for them, I'm willing to trust them. For now. But anything happens, I'm holding you responsible." Colonel Haley said as she left.

"Your new boss?" Barry asked.

"Yup." Kara muttered. "Be careful around Haley, she's a hard-ass and by-the-book."

"Got it." Cisco nodded. "So, what happened?"

* * *

_**Three months ago** _

"Are you sure it's here?" Supergirl called out as she was flying in the air, using the special suit from Lena.

"The coordinates are a match." Brainy said, flying next to her with his Legion ring.

"Be careful. We don't know what are we dealing with." Alex called out from DEO.

"Don't worry, Director Danvers, we will be careful." Brainy assured as they neared the ship. "It's ancient. Coluan…"

"Like your ancestors?" Kara asked.

"Yes." Brainy said. "It's fascinating…"

Suddenly, an alert bleeped. "Oh, no." Alex panicked.

"What is it?" Kara called out.

"Uh, someone fired a missile from the ground." Alex said.

"Lockwood and the Children of Liberty." Kara realized. "Can you intercept it?"

"I can't make it in time." Alex said. "And you can't stop it, it's irradiated with red sun."

"No but I can slow it down." Kara said as she dove towards the missile, trying to slow it down.

"I'm downloading the data." Brainy said as he plugged into the ship's computer and quickly downloaded the data into his brain.

"Brainy! I can't hold it for much longer!" Kara cried out.

"Got it!" Brainy said as he flew away from the ship, while Kara let go of the missile as it blew the ship up.

* * *

"Liberty! Liberty! Liberty!" Children of Liberty cheered before DEO agents surrounded them, with Alex in charge.

"Benjamin Lockwood, you are under arrest for acts of terrorism and threatening U.S. civilians!" Alex yelled.

* * *

_**DEO** _

"Mr. President." Alex greeted the U.S. president Plastino.

"Director Danvers." The president shook his hand with her. "Thank you for apprehending this terrorist called Agent Liberty."

"His followers are in disarray but we're working on hunting them down." Alex assured.

"Good to know. Anything else I should know about?" The president asked.

"We're working on protecting both alien and human citizens here, I can assure you." Alex said.

"This radical movement Mr. Lockwood led, has been quite provoking." The president shivered. "And then there is still this Manchester Black…"

"We're working on finding him. Hopefully we can stop him before he causes more trouble." Alex said.

"I'm certain he will try to go after Lockwood, if what you've said, is true." The president said.

* * *

Brainy was in the training room, sparring with Nia, who was blindfolded as they exchanged blows.

"Excellent. Your precognitive abilities are progressing." Brainy said before he hit her in the back as she fell down.

Nia put down the blindfolds. "I'm still too slow."

"It's not about speed or strength. It's about instincts." Brainy said.

"I told you, I can't control…"

"Nia. If you don't trust in yourself, you'll never win. There's no room for doubt." Brainy assured her. "Again!"

Nia took a breath as she put on the blindfolds, again sparring with Brainy, landing few hits as she predicted his attacks. "Good!"

Suddenly, he was knocked down as he groaned before he suddenly hit Nia hard as she groaned upon falling down. "Brainy!"

Suddenly, Brainy came to. "Nia! Oh, dear, I'm so sorry." He held her face gently. "I didn't mean to, are you OK?"

"It's just a bruise, I'm fine. I think I need a break." Nia said.

"Yeah, I think that's a good idea." Brainy nodded as she left, while he was starting to shake and have a seizure.

" _Collect… collect… collect…_ "

Suddenly, he came to as he shook his head as Nia neared him. "Brainy. Are you OK?"

"I'm fine, Nia. I'm fine." Brainy said, although it sounded like he was trying to convince himself, rather than her, wondering what was happening to him.

**Notes for the Chapter:**

> So, what do you guys think?
> 
> Please review and let me know if you have enjoyed this and want for me to continue.


	3. The Elite

**Summary for the Chapter:**

> Kara and Superfriends face off with Manchester Black and the Elite.

**Notes for the Chapter:**

> Disclaimer: I do not own DC Comics or the CW TV shows Arrow, The Flash, Legends of Tomorrow, Supergirl or any other characters or elements pertaining to the mentioned franchises.

J'onn came to visit Manchester in prison. "It's been weeks and now you agree to see me? Why now?"

"Well, let's just say prison has changed me." Manchester smiled.

"Look, you lost someone. I know how that feels. Let me help you." J'onn tried to plead with his friend. He was a good man but his methods of seeking justice were too extreme.

"You think I'm good deep down, huh?" Manchester chuckled. "Well, it's a bad time to be a good man. Take you, for instance. If it weren't for your bloody promise, I believe you could solve all the world's problems. You just need… motivation."

Next thing J'onn knew, he felt a jolt of electricity as he fell down as an Asian man disguised as a guard with a purple hat neared Manchester.

"This is Hat. We go way back." Manchester said.

"Hello." Hat chuckled.

"I wanted to thank you in person." Manchester smiled as he bent towards J'onn. "I was thinking small. Hellbent on getting Lockwood. Petty revenge. But I've got bigger fish to murder. And you can't stop me, old man."

"Don't do this." J'onn begged.

"Thanks for the chat, mate. Cheered me right up." Manchester said as he and Hat left the prison, with Manchester and Hat fighting through the guards. Supergirl flew in, trying to intercept Manchester but he and Hat teleported.

* * *

_**Fortress of Solitude** _

" _This Earth First Liberty crowd, they hurt aliens._ " Manchester announced on live feed. _"And what, they don't think we'll hurt them in kind? Why? Because Supergirl says that's not the way? Supergirl's like a folktale. In theory, comforting, noble. In reality…"_ He scoffed. " _Ill-equipped and clinging to ideals long past. When they go low, she goes high. We put them six feet lower. We're through giving these devils the benefit of the law. Supergirl is done. This is the era of the Elite._ " On the screen appeared his two compatriots, the Hat and Menagerie.

The feed ended.

"He's taunting me." Kara said.

"What makes you think that?" Nia asked.

"You wouldn't see it with a naked eye but in the transmission was coded an image. A map only I could see." Kara said.

"Superliminal stimuli embedded in structural light." Brainy realized. "I don't want to be impressed but…"

"Where does he want to meet?" J'onn asked.

"Manchester, England. Guess he wanted a homecourt advantage." Kara said. "We don't have much time." Then they saw how hesitant J'onn was.

"What is it, J'onn?" Nia asked.

"All I've wanted to do since my father died was to honor him." J'onn said. "And live by his example."

"And you have." Kara assured.

"But I'm struggling. There's a duality in me that's in war." J'onn sighed. "I want to be a man of peace just like my father but every fiber of my being is fighting against that. Being a manhunter was a part of my nature."

"And you're considering taking up the sword?" Kara asked.

"I made a personal vow. I wouldn't take that lightly." J'onn said.

"Well, if you choose to join the fight to bring the Elite to justice, I'm sure your father would understand. Even Myr'nn joined the fight against Reign." Kara assured before the comms in the Fortress went off and monitor turned on. "Alex?"

"We have a problem." Alex said. "I think I know where they are going. Lockwood tells us that Lex had prepared a military satellite that _could_ , if deployed, blow up any alien spacecraft that would want to fly towards Earth. It's something Cadmus had been working on for years with Mercy and Otis Graves."

"That's where Manchester is heading." Kara realized.

"I'm coming with you." Nia said.

"Nia, are you sure?" Kara asked.

"She's ready." Brainy assured.

* * *

_**Devil's Tower, Wyoming** _

Manchester, Menagerie, Morae and the Hat entered the base before facing Supergirl and J'onn.

"How did you know where to find us?" Manchester asked.

"Fish and chips and tracking devices." Supergirl quipped.

"You're still outnumbered." Menagerie said before, much to their surprise, Brainy and Nia, now dressed as Dreamer showed up.

"You have the Elite, I have Super-Friends." Supergirl said.

Manchester chuckled. "Right." The Morae turned invisible, while Hat pulled out a Tommy gun and Manchester fired with his rifle but Supergirl was unfazed. Hat opened fire at the soldiers but J'onn rushed to help them as he phased them into the lower level to avoid the bullets as Hat chased them.

Supergirl was knocked back as Menagerie attacked with her snake symbiote.

"Oy, go after the Martian." Hat said as he pulled out from his hat an axe, while Manchester ran into the lower level.

Menagerie was about to finish Kara off but Nia used her powers to blast her back, amazed by using her powers for the first time. "Rad." Nia laughed.

"Rad." Kara smiled.

Brainy and Hat exchanged blows before Brainy knocked him down. He smiled at Nia in pride and Hat used the distraction to punch him in the face.

* * *

J'onn evacuated the soldiers before Manchester shot him from behind with a blaster. "Go on. Turn the other cheek." He picked his axe, about to finish J'onn off before Alex jumped down from above and fired, forcing Manchester to drop his axe. Alex jumped down and picked a baton, exchanging blows with Manchester. He knocked her back before Alex did a Hurricanrana, slamming him to the ground.

"You OK?" Alex asked as J'onn nodded.

"Alex?" Kara asked, as she noticed her.

"Stop the launch, we'll handle it." Alex said before Manchester got up, while Alex and J'onn engaged him.

* * *

Brainy and Nia were exchanging blows with Hat, who teleported himself.

Suddenly, Nia's precognitive powers came to aid as she dodged a punch from behind and kicked Hat back as he was trying to surprise her by teleporting behind her. "How'd you know where I-"

"Dreams." Nia growled. She threw a left hook but Hat teleported himself.

Brainy looked around, waiting before he raised his hand as Hat appeared above him. Brainy grabbed him by his leg and slammed him to the floor. "Differential calculus."

Hat got up as Brainy kicked him back and then he sent a flurry of punches in precise spots, knocking him down.

"Brainy."

Brainy suddenly came to as Nia stared at him in shock before he realized what he did. He had always shown restraint during fight, so what was happening to him?

"Wait. Where's the Morae?" Brainy realized.

* * *

The Morae was at the console, about to launch the satellite but Kara used her heat vision beams, knocking him down.

* * *

J'onn and Manchester were exchanging blows but J'onn knocked him down before pummeling him as Manchester ended up with bruised and bloodied face, laughing. "There you are, J'onn J'onzz. Nice to finally meet you."

"I know why you called me now. You have a death wish." J'onn said. He knocked Manchester out.

* * *

Later, the army and DEO apprehended Manchester as Alex was holding an icepack on her head.

"How's your head?" Kara asked.

"Don't worry about it." Alex said. "They're all going somewhere they can never hurt anyone, ever again."

"Hey, Kara, can I talk with you for a moment?" Nia asked as Kara followed her.

"What is it, Nia?" Kara asked.

"Has Brainy ever been… violent?" Nia asked.

"What do you mean?" Kara blinked.

"Well, when we were training, he kind of snapped and hit me hard." Nia said. "And today, it was like he… he didn't hold back. You should've seen how he beat up the other guy."

Kara was confused. "That doesn't sound like Brainy. He usually fights with a lot more restraint."

"Frankly, I'm worried about him." Nia said.

"Me too." Kara admitted, looking at Brainy, who was examining some of the data on the tablet from the base. "Are you OK?"

"I'm fine, Kara. Why?" Brainy asked.

"Usually, you're not so violent but you've been acting odd lately. What's going on?" Kara asked.

"Don't worry about me. I'm fine, really." Brainy said.

"You sure?" Kara raised her brows and Brainy nodded. "Brainy, you know we're here for you, right?"

"I appreciate it but I'm fine. Really." Brainy assured as he walked off.

"You can't stop me."

Brainy paled as he recognized the voice. He turned around to see a bald man with a beard and in black suit. "Lex Luthor…"

"What?" Brainy blinked before in front of him instead of Lex appeared Kara. "What about Lex?"

"Uh…" Brainy trailed off. "Just that he always finds a way to trouble us. That's all."

Kara nodded but narrowed her eyes. Something was happening with her friend.

* * *

_**CatCo** _

James was leaving his office before in front of him appeared a man with a ski mask in black jacket, who pulled out his gun and fired as James felt sharp pain in his chest as he stilled and looked down before he fell to the floor, bleeding out, while the shooter walked away.

**Notes for the Chapter:**

> Frankly, as good villains as the Elite was, I think they could've been beaten more easily, plus don't forget that Brainy is not exactly himself right now.
> 
> So, what do you guys think?
> 
> Please review and let me know if you have enjoyed this and want for me to continue.


	4. Manhunter's struggle

**Summary for the Chapter:**

> Manchester escapes, while Alex and Lena deal with arrival of James's sister after he had been shot and J'onn struggles with his ideals and convictions to stop Manchester.

**Notes for the Chapter:**

> Disclaimer: I do not own DC Comics or the CW TV shows Arrow, The Flash, Legends of Tomorrow, Supergirl or any other characters or elements pertaining to the mentioned franchises.

_**National City General** _

Kara, Brainy and Nia were in the reception, waiting before Lena burst in, hugging Kara tightly. "Oh, Kara, thank God you're OK. I heard what happened at CatCo and I wasn't sure."

"No one else was hurt, just James." Kara assured.

"Is he alright?" Lena asked.

"They're about to operate but… his spine was badly injured. We don't know what's gonna happen." Kara said.

"OK, where is he?"

"He's upstairs, but they said he can't have visitors yet."

Lena's eyes narrowed. "Well, I'm not a visitor, I own this hospital."

Brainy held Lena by her shoulder. "Little boxes." Lena nodded, getting the message. Take it easy. She left as Brainy turned to Kara. "What exactly transpired?"

"All I know is that he was shot in his own office from behind." Kara said. "They used a hollow point. It… splintered."

"Who would do something so horrible?" Nia whispered.

"Someone without a soul." J'onn said as he entered. "This has to be Manchester Black. In the prison, he threatened me. He swore to come after me and my family, everyone I care about. Seems he started with James."

"We better make sure he can't escape." Kara said.

"I told Alex already. They'll keep an eye on him." J'onn assured. "Stay with James. This needs to end right now."

"No. I-"

* * *

_**DEO** _

Agent Vasquez was putting the Fifth Dimension hat into a box before suddenly, it teleported. "What the-"

* * *

Manchester Black and the Hat were in their cells before the Hat got back his hat and they both smirked before there was an explosion in the prison level.

* * *

_**Later** _

"How the hell did Manchester and the Elite escape?" Kara demanded.

"Someone tampered with the power dampeners on that magical hat. That's how they got out." Alex said.

"Who would do something like this?" Nia asked.

"I don't know. We might have a mole in DEO. Colonel Haley is not going to like it." Alex wiped her face as she turned to Brainy.

"I'm on it, Director Danvers." Brainy said as he left.

"Where did he even go?" Kara wondered.

Suddenly, J'onn had a vision of Myr'nn's death and Manchester betraying him, realizing he was linked to Manchester somehow. "I think I know where he is. He's done something terrible, I can sense it."

"I'm coming with you." Kara said.

"We should check in on James. Nia, come on." Alex said, picking her car keys as Nia followed her.

* * *

J'onn and Supergirl were deep in the mountains as they looked around. "What is this place?"

"This is where my father died." J'onn said. He landed on the ground before a circle of fire formed around him. "Supergirl!"

"I'm on it." Supergirl used her freeze breath to extinguish the flames but suddenly, everything around J'onn slowed down as he faced Manchester, who held in his hand the Staff of H'ronmeer.

"Hello, J'onn." Manchester said.

"How are you capable of this?" J'onn demanded.

"When you broke into my mind to stop me from killing the Lockwood brood, you opened up a motorway." Manchester smirked as he tapped himself on the temple of his head. "It goes both ways. So, whenever you poke around in my mind, I can poke around in yours. So, I did." He lifted the staff. "And look what I found. Your people's most powerful weapon."

"You don't know what you're toying with." J'onn warned. In wrong hands, that staff would cause mass destruction.

"Oh, but I do." Manchester said. "I dug deep into your mind. And the ground. You call yourself a man of peace, Martian, but your god was one of wrath." The staff in his hand glowed with energy.

J'onn glared. "You burned my father's grave to teach me a theology lesson?"

Manchester laughed. "You forget H'ronmeer's punishments. You're a hypocrite." He slammed the staff to the ground. "Wake up, man! It's time you followed the true righteous path. And we can put a stop to the hate that's burning up this world, just like it burned up Mars. We can stop it together."

Kara flew in through the barrier but Manchester had managed to teleport himself. "I heard everything." She turned to J'onn in worry. "J'onn, what did he mean, when he said 'the punishments'?"

* * *

_**DEO** _

"Do we know who compromised DEO's security, agent Dox?" Colonel Haley asked Brainy, who shook his head.

"Whoever did this, was good. Very good. It might have been an inside interference." Brainy said.

"You believe we have another mole in DEO?" Colonel Haley demanded.

"After Jensen, I wouldn't be surprised." Brainy nodded. "I checked and the code does resemble one of Lex's old-"

"It can't have been Lex or Mercy Graves or Otis." Colonel Haley shook her head.

"I know. I'm working on it." Brainy said. "But they also stole sun-eaters. They can work as batteries."

"Find out whoever's responsible for this. The last thing we need is DEO being compromised." Haley said and Brainy nodded, walking off before he faced Lex again.

"There's nothing you can do to stop me." Lex taunted.

"What are you up to?" Brainy glared.

"We're playing chess. And right now, I'm a step ahead of you." Lex sneered.

"We're gonna find him, agent Dox, don't worry." One of the agents assured as he felt her hand on his shoulder. Brainy glanced at her before turning to Lex, who had disappeared. How was he doing this?

* * *

_**National City General** _

"Mr. Olsen is stable. We were able to remove a significant amount of shrapnel from around his cervical vertebrae but I've never seen a normal bullet cause this much damage." The doctor said. "We've placed him into a medically-induced coma."

"To reduce swelling, of course." Alex nodded.

"There are going to be some decisions to make. Who's the next of kin?" The doctor asked.

"Well, there's no family present but I could act as James's-"

"Sorry, but without a court order, I'm afraid I cannot-"

"Look, I'm FBI and I have extensive medical train-"

"I appreciate what you're trying to do but I'm afraid I cannot let you—"

"I'm the next of kin." Alex, Lena and Nia turned to see a dark-skinned woman with long hair enter as they saw how she resembled James, realizing it was his sister. "Sorry, I just got off a red-eye. I'm Kelly Olsen."

"James's sister." Lena realized.

Kelly nodded as she turned to Alex. "You said you're FBI, right? You must be Kara's sister."

"Yeah, um, I'm Alex." She offered her hand.

"Lena Luthor. James's girlfriend." Lena introduced herself.

"It's nice to finally meet you." Kelly smiled. "I wish it were under better circumstances." She turned to the doctor. "I'd like to see James, right away."

"Absolutely."

"And these people are family too. Make sure they have access." Kelly turned to Alex, Lena and Nia.

"Lena, is there a way to help him?" Alex asked.

"I've been working on a serum that may be able to heal James's injury but it's untested. I can't guarantee it will help James and even if it will, there may be side effects that we cannot anticipate." Lena said.

"I'm sorry but I'm not ready to trust a Luthor, not after what your brother has done to mine." Kelly protested.

"Kelly, I care about James as much as you do and I want to help-"

Kelly shook her head. "No. I'm afraid my answer is 'no'."

Lena sighed as Alex dragged Kelly away, lowering her voice. "Kelly, listen, I understand you don't trust Lena Luthor but believe me, when I say she wants to help your brother as much as you do."

Kelly sighed. "Even if I trusted her motives, I'm not ready to trust whatever she has prepared."

"Just think about it, OK?" Alex insisted as Kelly took a breath before turning to the doctor.

"Can you take us to James, please?"

"Of course."

* * *

_**J'onn's office** _

J'onn was in his father's robes, on his knees, meditating. " _Father. Hear me. I am so lost._ " He whispered in Martian.

Suddenly, he saw rotten zombie forms of Alex and Kara.

"We all died, J'onn, while you stood idly by." 'Kara' said and J'onn breathed out, terrified.

"You just sat there and you waited." 'Alex' added, circling around J'onn who shivered in fear. "And you prayed and you sat there."

"While you came for us!" Both of them yelled.

"You're not real." J'onn got up, shaking his head in denial.

"We are."

"So real."

"Manchester, show yourself!" J'onn snapped, closing his eyes.

"We're the ones you couldn't save. Who you wouldn't save. Just like your own daughters!"

The zombie apparitions grabbed J'onn by his throat as he screamed, leaning onto the chair. "Kara! Alex! No!"

"J'onn! J'onn!" Kara shook him as J'onn opened his eyes, terrified before he saw normal Kara and relaxed, breathing out. "Hey, it's me. It's OK. It's OK." J'onn got ahold of himself as he straightened himself. "What happened?"

"Manchester was trying to show me what would happen if I continued to idly sit by." J'onn said. "I have left you and Alex alone to face dangers." He took a breath, pacing down his office. "Is choosing a path of peace worth it if it means I could lose everyone I care about?"

Kara sighed, folding her arms. "After what happened on Krypton, the way my mom stood by and did nothing I've always sworn that if I can act, I will. But until you took your vow of peace, I didn't truly understand that simply by standing with someone, you can make them feel braver." She put her hand on J'onn's shoulder. "J'onn, the only reason Alex and I can face danger the way we do is because we know you're standing by us. In whatever way you choose."

J'onn smiled and nodded. "Thank you. What should we do now?"

"Well, clearly Manchester wants you to hunt him, so he can exploit your psychic connection and attack you and we've just been playing into his hands. So, maybe the best thing we can do now is let him come to us." Kara suggested before lights flickered. "What's going on?"

"A power surge. It's Manchester." J'onn used his powers to locate him. "He's at the dam. With the staff's powers, he could wipe out the whole city."

"Let's go." Kara said.

* * *

_**DEO** _

"We're under attack! Someone's overridden our security protocols!" Vasquez said.

"Who? Why? Where's Brainy?" Another agent demanded.

* * *

_**National City** _

Supergirl and J'onn flew to the dam, facing off Manchester Black.

**Notes for the Chapter:**

> I know that Lena and James did break up earlier because of Lena trusting the government with her Harun-El project and James's issues with her handing over her research to Colonel Haley but let's pretend that they didn't, since to be honest, that didn't make much sense to me that Lena would FULLY trust the government with her experiments.
> 
> So, what do you guys think?
> 
> Please review and let me know if you have enjoyed this and want for me to continue.


	5. Manchester's fall

**Summary for the Chapter:**

> Kara and J'onn face Manchester one last time as a mysterious assailant targets James and Lena.

**Notes for the Chapter:**

> Disclaimer: I do not own DC Comics or the CW TV shows Arrow, The Flash, Legends of Tomorrow, Supergirl or any other characters or elements pertaining to the mentioned franchises.

Supergirl and J'onn were in the generator room of the dam, looking around.

"Manchester!" J'onn called out.

"Well, well, it's about time." Manchester said, standing on a catwalk above, wielding the Staff of H'ronmeer. "Come and get it, Martian of peace!"

Supergirl fired heat vision beams but Manchester used the Staff to deflect as the blast destroyed a nearby wall.

"The dam's cracked." Supergirl said. "He's gonna flood the whole city."

"Go. This war is mine." J'onn ordered.

Supergirl flew away and used her freeze breath to stop the leaking water from the dam but soon enough more water burst through the cracks. "Damn it!" She used her heat vision to seal the cracks.

J'onn phased through the floor as Manchester fired a blast from the Staff before nearing Manchester and used a wrench to block as Manchester attacked with the staff.

"Stop this madness! You'll kill thousands of innocent people!" J'onn said.

"This world is already tearing itself apart. If you want to stop that, don't fight me. Join me." Manchester said with an imploring look.

"Never." J'onn growled before he attempted to strike Manchester. Manchester ducked as J'onn hit a gas tank and as it leaked from it, it blinded J'onn. Manchester knocked J'onn back and dodged, when J'onn swung his wrench.

* * *

**_National City General_ **

Lena entered the operation room, when it blacked out and ordered the doctors to leave before she pulled out the Harun-El serum, about to inject James.

* * *

**_National City dam_ **

"If you don't stand up and fight, you'll lose everything. Again." Manchester said as he used the Staff to show J'onn the vision of his daughters being murdered by White Martians.

"No… no!" J'onn yelled as he lunged forward before the vision disappeared and Manchester smirked. J'onn screamed in anger, turning into a Martian and pulling the Staff towards him before stabbing Manchester in the heart with the tip of the Staff.

Manchester smiled as he saw the vision of his fiancée. "You're beautiful." In a matter of seconds, he evaporated as he was glowing until he faded into nothingness.

Kara flew in, looking around. "J'onn. Where's Manchester?"

J'onn sighed as she stared at him in worry. "Let's go see James."

* * *

**_Later, National City General_ **

"Mom was quite freaked out." Kelly said as they left James's hospital room.

"He's going to recover soon. Don't worry." Lena assured.

"What did you inject him with?" Kara asked and Lena was silent.

"It was… an experimental drug." Lena said after a moment.

"Untested?" Alex blinked. "Lena, what if there—"

"I know, Alex." Lena nodded. "Look, if something happens to him, I'm taking full responsibility."

"You did what you could. I'm glad you at least tried to save my brother." Kelly said. "Thank you."

* * *

J'onn stared at a nearby wall outside James's room. "J'onn… the whole city is OK because of you." Kara assured.

"But at what cost?" J'onn wondered. "Manchester is dead."

"I know you're trying to honor your father's code, but what happened today doesn't change who you're trying to be." Kara said.

"I don't know who that is, Kara. One thing I do know." J'onn sighed. "I am not a man of peace."

Kara held J'onn's hand, not sure what to say.

* * *

"Thank you for looking out for my brother." Kelly said. "I don't know what I—"

"If it had been Kara, would you have done any differently?" Alex asked and Kelly smiled.

"You're a good person, Alex. A hard-ass but a good person." Kelly said.

Neither of them noticed that they were holding hands the whole time, while walking down the corridor until they pulled away as Alex's phone rang. "Sorry. I gotta take this."

* * *

**_Later, DEO_ **

"Who stole Myriad from us?" Alex asked as Brainy filled her in.

"I don't know but… it might be Lex Luthor." Brainy said.

Alex scoffed. "Brainy, that's impossible, Lex is imprisoned on Stryker's Island and under constant surveillance."

"Agent Dox, can you confirm your allegations? Because we have no time on wild goose chases." Colonel Haley demanded.

"The code used to hack us is an old LexCorp code." Brainy explained.

"Unless it's Lockwood or someone from Lex's old associates, it's not possible." Alex said.

"Keep digging. We must be certain." Colonel Haley said. "Agent Vasquez said you were missing for half an hour. Where have you been, agent Dox?"

"Searching for clues in places that aren't on the blueprints of the base." Brainy said and Colonel Haley narrowed her eyes before nodding as she left.

"Brainy, are you OK?" Nia asked. "You've been kind of on edge lately."

"I… I'm honestly not feeling myself. I don't know what's happening." Brainy admitted.

* * *

_**L-Corp** _

"Thank you for accompanying me, Kara." Lena said as Kara accompanied her into the elevator.

"Anytime." Kara said as they went out. "Look, Lena, if there's anything I can do for you—"

Kara suddenly screamed as she was shot with some beam in her shoulder and she fell down. Normally, it wouldn't hurt her but she felt burn. Well, it was luck that it hurt, otherwise Lena would probably put together Kara's secret as they faced a man wearing an armor and a helmet.

"Kara, are you OK?" Lena cried out as she knelt towards her.

"Lena Luthor. You have something my employer wants." The man in a helmet said as Lena paled, while he aimed at Kara and Lena.

**Notes for the Chapter:**

> So, what do you guys think?
> 
> Please review and let me know if you have enjoyed this and want for me to continue.


	6. Rip Roar

**Summary for the Chapter:**

> A hi-tech assassin kidnaps Lena, attempting to create a global catastrophe.

**Notes for the Chapter:**

> Disclaimer: I do not own DC Comics or the CW TV shows Arrow, The Flash, Legends of Tomorrow, Supergirl or any other characters or elements pertaining to the mentioned franchises.

"Leave her alone." Lena stepped up in front of Kara protectively.

"Lena, no!" Kara exclaimed.

"I'll give you whatever you want, just don't hurt her." Lena begged.

The man considered for a moment before from his backpack protruded some metal tentacles, ensnaring Lena and taking her away.

"Lena!" Kara cried out.

* * *

_**Later, DEO** _

"Is that him?" Alex asked as she showed Kara the photo.

"Yeah." Kara nodded, once her shoulder had healed before she read the profile. "An assassin?"

"We don't know his real name but his codename is Rip Roar." Brainy said. "Looks like another hired gun, who was paid to settle another beef with Lena. He's very notorious on the dark web."

"Who knows what he wants with her? Harun-El experiments? L-Corp technology?" Alex wondered.

"I don't know but we need to find this Rip Roar before he hurts Lena and anyone else." Kara said.

"I think I might have an idea." Brainy said as he hacked into L-Corp servers. "This is from an hour ago."

On the footage was Rip Roar with Lena, forcing her to give him access to the labs as he used his tentacles to steal some giant device.

"What did he steal?" Kara asked.

"Some kind of a transmitter. A signal booster. With the right expertise, you could basically take over the worldwide broadcast." Brainy said. "Who knows what he could use that for."

"I think you and I both know what I would use it for." Lex gloated and Brainy shivered, ignoring Lex.

"Lex… this could have Lex's fingerprints." Brainy said.

"What makes you think that?" Nia asked.

"I've detected suspicious activity from Lex's older accounts. It's possible he may have access to his resources from prison." Brainy said.

"That's impossible, they have him under constant surveillance." Alex shook her head.

"With Lex Luthor, anything is possible." J'onn said as Alex sighed.

"OK, I'll call the warden on Stryker's Island, get him to check in on Lex. We need to find a way to track down this…" Alex trailed off.

"Rip Roar." Brainy said.

"Rip Roar." Alex nodded.

"The moment this Rip Roar turns on the transmitter, we can locate the signal." Brainy said.

* * *

_**Elsewhere** _

"Why are you doing this? What do you want?" Lena asked as she was helping Rip Roar build the transmitter.

"A better world." Rip Roar said cryptically.

He didn't notice that Lena had been typing away something on the computer.

* * *

_**DEO** _

"From what Colonel Haley said, he also stole a fusion cannon and a particle amplifier. It's a revamped version of Lex's Marathon Laser." Brainy said. "With the right expertise, it fires an energy beam 100 times hotter than the center of the sun. If he shoots you, he could weaken you."

"Can we detect it?" Alex asked.

"I've been trying to but it's not easy. The weapon was designed to be undetectable." Brainy shook his head before he got a signal. "Well, well, well… I know where he is. He's in Lake Vostok. It's the largest subglacial lake on the planet. Now, I'm no supervillain but if I were, and I was right over an Antarctic lake with a weapon designed to fire a beam hundred times hotter than the core of the Sun…"

"You're saying he's gonna melt the ice cap around Lake Vostok?" Alex realized and Brainy nodded.

"If he did that, it would unleash a flood unseen since the time of Noah's Ark." J'onn said.

"And how did Lex get past our security measures here? Why did he steal Myriad?" Kara asked.

"I'm not sure." Brainy admitted.

"Alright, we'll check in on Lex once we stop Rip Roar." Kara said.

* * *

_**Lake Vostok** _

Supergirl and J'onn entered the facility and saw dead guards before they saw Rip Roar aim the laser at the ice wall in front of him.

"Rip Roar, no!" Supergirl yelled.

Suddenly, the facility tremored as the ice cracked as it created a tidal wave.

* * *

_**DEO** _

"Status?" Alex asked as the alarm blared.

"A massive eruption in the Antarctic water table has sent shock waves east and west, resulting in an unprecedented number of sea swells." Brainy said as he showed Alex the readings on the monitor. "Based on the seafloor pattern and the Antarctic Circumpolar Current, the biggest is set to make landfall on the Pacific coast in under an hour."

"Which part of the Pacific coast?" Alex demanded.

"All of it." Brainy said grimly as Alex paled.

* * *

_**Lake Vostok** _

Rip Roar was on the run before Kara knocked the cannon off his hand. "Leaving so soon?" Suddenly, the ice cracked as she stared in horror before J'onn restrained him. "What have you done?"

"Kara, do you copy?" Alex called out.

"Alex, we have Rip Roar but he punched a hole in the lake." Kara said.

"We know. The eruption just sent a tidal wave our way." Alex said.

"We can deal with the swell, Supergirl. You and J'onn need to seal that geyser, or else we'll have bigger problems than a wave." Brainy said.

"What do you mean?" Kara demanded.

"That geyser is pumping out three cubic miles of water every second. At that rate, every coastal city in the world will start flooding in 12 minutes. The loss of life could be in the billions." Brainy explained.

"How do we stop that wave?" Alex demanded.

"It's too late. You can't stop it." Rip Roar said.

"Not alone, we can't." Kara said before she pulled out a breach device.

* * *

**_S.T.A.R. Labs, Earth-1_ **

Cisco and Barry were in Cortex, tracking Cicada before suddenly, Kara entered. "Barry. I need your help. Right now."

**Notes for the Chapter:**

> So, what do you guys think?
> 
> Please review and let me know if you have enjoyed this and want for me to continue.


	7. Brainiac awakens

**Summary for the Chapter:**

> After preventing a catastrophe, Brainiac awakens in Brainy.

**Notes for the Chapter:**

> Disclaimer: I do not own DC Comics or the CW TV shows Arrow, The Flash, Legends of Tomorrow, Supergirl or any other characters or elements pertaining to the mentioned franchises.

**_National City, Earth-38_ **

Nia, dressed as Dreamer, was at the shore, evacuating the people. "Everyone, run! Move! Get to the high ground! Go!" She took a breath, facing the tidal wave. "Brainy… I hope this works."

Nia summoned her powers and created and energy wave, while Alex and the DEO was coordinating the evacuation.

Kelly was running down the street as one of the cranes was falling down on her.

"Kelly!" Alex exclaimed, running towards Kelly and tackling her out of the way before the crane would crush her. "You OK?"

"I'm fine." Kelly nodded. "Thanks, Alex."

"We need to get out of here, go, go!" Alex helped Kelly on her feet as they ran off.

* * *

**_Lake Vostok_ **

"Caitlin, can you freeze it?" Kara asked.

"We don't have time for that!" Caitlin protested.

"The geyser's pushing up the tidal wave! We need to find a way to pull it down!" Barry ordered.

"Like a whirlpool?" Kara realized.

"J'onn, Kara, fly around the facility! I'll run around and hopefully we can suck the water in! But if you guys get suck into the vortex, you'll suffocate!" Barry said.

"Well, then, we better keep our cool!" Kara said as she and J'onn flew around the geyser.

"Caitlin, the moment the geyser gets suck in, seal it off!" Barry ordered and Caitlin nodded as Barry sped around the geyser.

* * *

**_National City_ **

Nia was using her energy projection powers, while Cisco was using his vibe blasts to slow down the tidal wave.

* * *

**_Lake Vostok_ **

As soon as the geyser was sucked in, Caitlin used ice beam to seal the geyser.

"It's over." Kara said.

* * *

_**National City** _

"The agents are helping with the evacuation." Alex said. "I'll head back to DEO. We need to find out what's going on."

"And I think we need to have a chat with Lex." Kara said as she flew towards Stryker's Island with J'onn.

"See you later." Cisco said as he opened a breach for Team Flash to get back into the city.

"Well, at least I didn't travel back in time because of tidal wave again." Barry quipped as they all laughed.

"I think I could use some ice cream. What about you?" Cisco said.

"Yeah." Caitlin smiled.

* * *

_**Stryker's Island** _

"There's no way he could've escaped." The warden said, accompanying Supergirl and J'onn down the corridor, opening Lex's cell as Lex got up, smirking.

"Supergirl. Mr. J'onzz. To what do I owe this visit?" Lex smirked.

Supergirl took a breath. "Mr. Luthor, have you been recently to DEO?"

"No. I assure you, I haven't left this prison in five years." Lex smiled as Supergirl turned to J'onn, who checked Lex's mind.

"He's telling the truth." J'onn said.

"If Lex was here the whole time, then who…"

* * *

_**DEO** _

Brainy was in the lab, trying to figure out why would Lex steal Myriad and a signal booster before he heard a maniacal cackling as he turned around to face Lex again. "No. No." He stepped back, shaking his head before firing a beam from his ring, obliterating Lex as he sighed in relief. "Finally. It's over."

"It'll never be over."

Brainy paled as he whirled around to face Lex again as he stepped back in horror. "H-How…" Lex laughed. "I killed you. You can't be here. I swear, if you hurt my friends—"

"You'll do nothing. Because you can do _nothing_." Lex gloated.

"No." Brainy stepped back, shaking his head and holding it. "No! Just leave me alone! Leave my friends alone!"

"With Myriad I will—"

"Never. I'll stop you." Brainy fired some energy blast from his hand but went straight through Lex.

"Brainy, what are you doing?" Alex demanded.

Brainy turned around to face her before turning to Lex again, who laughed. "Poor Alex."

"No!" Brainy glared, pointing at him. "Leave my friends alone!" He whirled on Alex. "Alex, run!"

Brainy glared at Lex. "I swear, if you as much as lay a finger on her—"

"Brainy, stop! Please, stop! There's nobody there, it's just you!" Alex cried out, tears filling her eyes as he turned to her.

Brainy snorted, shaking his head. "No. That's impossible." He turned around only to notice that "Lex" had vanished. "He… he was right here. I saw him. He must have used some device the instant you entered—"

"No." Alex shook her head, staring at her friend in worry. "I've been watching you for a while and the whole time you've been shouting at the air. Stop!"

"No. No, he must have used something to—"

"Brainy, it's gonna be OK, we're gonna figure this out, OK?" Alex said before her comms went off.

" _Alex, is Brainy there?_ " Kara called out.

"Yeah. And there's something wrong with him, he's been talking with Lex…"

" _But he's not really there, is he?_ " J'onn realized as Alex nodded. " _We just checked in with Stryker's Island. Lex hasn't left the prison and there's no way he could've compromised DEO somehow, they've had him on constant surveillance the whole time. I'm not sure what's going on with Brainy but…_ "

"It's all in his mind." Alex realized. "What's happening to him?"

" _I think we have a pretty good idea. Alex, run. Get as far away from him as possible._ " Kara said as Brainy was falling on his knees, sobbing, as if he was having a breakdown.

Alex neared Brainy, holding him by his shoulder. "Brainy. It's gonna be OK. We can help you."

Suddenly, Brainy got up as he stopped sobbing and he turned around to face Alex and as she looked into his eyes, the look he was giving her was chilling, as she immediately realized that there was something very off about him before she realized that she had seen that cold look before as she paled, realizing who was she facing. "Oh, my God… you… no… not you. It can't be…" She shook her head.

"You're in my way." "Brainy" said darkly as Alex breathed out, horrified.

"Brainiac. What do you want?" Alex demanded, trying to keep a straight face and taking a breath.

"What I've always wanted." Brainiac said.

"Let Brainy go." Alex ordered.

"Brainy? What a sentimental petulant name." Brainiac said, disgusted. "Emotions held me back. They don't anymore."

Alex reached for an alarm button in her remote but Brainiac grabbed her by her throat and squeezed as Alex choked. Brainy then heard footsteps as Alex's vision blurred and there was 'crack' heard before Brainy let Alex go as she lifelessly slumped to the floor and Brainy walked away.

"Alex? Alex!" Nia rushed to the armory but gasped in shock at seeing Alex lying on the ground and she broke down in tears.

* * *

As soon as they saw the footage and debriefed Team Flash, Barry stared in shock, unable to believe that Brainy would do something like this.

"It must have been that Coluan ship. Brainy is from Colu. Plugging into it must have rebooted him somehow." Kara said.

"Can we reverse it?" Caitlin wondered.

"I don't know. We'd need to access the information from the Fortress, assuming Brainiac doesn't count on it." Kara said as Nia was in the corner, apparently still in shock with J'onn comforting her.

"I know it's hard to accept it." J'onn said.

"That wasn't Brainy. It can't have been him…" Nia whispered, on verge of tears.

"We know, Nia." J'onn assured her.

"How are gonna save him?" Nia wondered.

"Honestly, I don't know." J'onn said. "But we may need to accept that we'll have to…"

"…kill Brainy?" Nia whispered. He was her friend and mentor and they became close to each other. He helped Nia embrace her powers and master them and on a certain level they cared for each other. "J'onn, you can't ask me to—"

"We won't force you to do anything you don't want to." Kara assured Nia, holding her by her shoulders.

After being found by DEO agents, when Rip Roar kidnapped her, Lena was in the briefing room with Supergirl and Nia.

"Is everything alright?" Lena asked.

"Lena, did Rip Roar hurt you?" Supergirl asked.

"No. I'm fine, don't worry." Lena assured.

"What did he force you to build?" Supergirl demanded.

"I'm not sure. Some kind of a signal booster. I don't know why." Lena said as Supergirl sighed. "What's going on?"

"Someone accessed Lex's accounts. We need to know if it was from here." Supergirl said as Lena sat at the computer.

"Apparently, someone did. Whoever did this, was very good." Lena said.

"It was Brainy. He's gone rogue." Supergirl groaned.

Lena looked confused. "Gone rogue? What do you—"

"That satellite two months ago, it compromised him somehow. Rebooted him." Supergirl explained.

Suddenly, the whole headquarters rocked. "What was that?" Lena demanded.

In the air floated some kind of a ship of a size of a skull.

* * *

_**National City General** _

James opened his eyes, as they turned pitch black with black veins forming as he clenched his fists.

**Notes for the Chapter:**

> So, what do you guys think?
> 
> Please review and let me know if you have enjoyed this and want for me to continue.


	8. Brainiac's fall

**Summary for the Chapter:**

> The heroes must stop Brainiac before he enacts his plan.

**Notes for the Chapter:**

> Disclaimer: I do not own DC Comics or the CW TV shows Arrow, The Flash, Legends of Tomorrow, Supergirl or any other characters or elements pertaining to the mentioned franchises.

"What is he doing?" Barry demanded as they saw the screen.

"He's reducing cities." Lena realized.

"That's what Brainiac did before." Supergirl said. "He collects worlds, drains them of their knowledge. That's how he stole Kandor. Mom told me."

"How are we going to stop him?" J'onn wondered.

"Well, we need to get onto that ship but he'll be ready for us." Supergirl said. Suddenly, on the computers appeared some strange alien symbols as Vasquez and other agents were in some kind of a trance, alongside Sherloque.

"What the hell?" Barry demanded.

"Vasquez. Wolf." Kara tried to shake the agents.

"Something's happened to them." Lena noted.

"He's downloading the knowledge from their brains." Kara realized. "That's what Brainiac did in one timeline, Mon-El told me."

"Then why are we not affected?" Barry wondered.

"Because you're metahumans and aliens." Kara said. "But Lena—"

"He must've downloaded everything from L-Corp already." Lena realized.

"We need to shut him down before they end up brain-dead. How are we going to get on that ship?" Kara asked.

"Uh, I think we got another problem." Cisco said as he saw on another screen which was not affected by Brainiac some drones walking down the street.

"Brainiac drones." Kara said.

"OK, we need to find a way to stop those drones and get onboard that ship." Barry said. "Do you think you can build something?"

"I'm on it." Lena said, running to the lab with Cisco.

* * *

_**National City** _

On the streets, people were running in fear as some skeleton-like robots were attacking them and attaching some wires into their skulls, presumably downloading their knowledge as they had suddenly glassy looks in their eyes, frozen like statues.

"We need to help them." Caitlin said, freezing the robots, while Ralph smashed them.

J'onn flew around, ripping apart the robots with his bare hands as on his eyes appeared black veins.

"James…" J'onn stared.

"I thought I could help." James offered as he ran off, trying to fend off the aliens.

* * *

Clark, Kara and J'onn were flying Barry, Cisco and Nia inside the ship as they looked around.

"It's Brainiac's design." Kara realized.

"Do you think we can stop Brainy?" Nia asked.

"I dread to think of what we might have to do." Kara shuddered.

They saw Brainy at the center on some throne with some tubes attached to his skull as he seemed… to be sleeping. With no hesitation, Kara ripped off the tubes as Brainiac screamed before Barry restrained him with some cables.

"This will not hold you for long. But long enough." Barry said.

"Brainy, this isn't you." Nia pleaded.

"Brainy is no more. I am Brainiac." Brainiac said on a robotic voice, turning into his normal form. "This world will be mine. Just like all others. I will continue my ancestors' mission."

"Brainy, you know this is wrong. We're your friends." J'onn pleaded.

"Friendship. Such a trivial concept." Brainiac said indifferently as some cables emerged from the walls, restraining Barry. Barry tried to phase out but felt some electricity surge through him, incapacitating him. Cisco attempted to blast Brainiac but a wall formed in front of Brainiac before it was flying towards Cisco, knocking him down. "I am this ship. You cannot defeat me."

"Brainy, you don't have to do this. Stop this, before it's too late." Kara pleaded.

"There is nothing you can do to stop me. I am in control." Brainiac said.

More drones appeared, attacking. Kara freed Barry and Cisco before Barry phased through the drones, short-circuiting them, while Nia and Cisco blasted them. Kara, Clark and J'onn punched through the drones before Kara punched Brainiac away but he got up on his feet, unfazed.

"Your affection is nauseating. Let's see if your brains can comprehend knowledge of thousands of worlds. I'd be surprised if you could take in one before your brains melt into goo." Brainiac used some telepathy as they all groaned, falling down as knowledge they had never known, was forced into their brains, having a headache of lifetime. Clark and Kara, struggling, used their heat vision as debris fell down from above, distracting Brainiac long enough to let them go.

Nia and Cisco blasted Brainiac, knocking him down. But as Kara, Clark and Barry engaged Brainiac, he predicted their moves, dodging before managing to knock them all back with precise strikes.

"Enough!" Kara snarled. She flew Brainiac out of the ship towards some bayou.

Brainiac got up, about to attack Kara again but then he noticed that he was covered in mud. "No… all this… activity… all this chaos…"

"It sucks, when you have to face things beyond your control, right?" Kara quipped.

Brainiac held his head, groaning before trying to attack Kara. Kara dodged before punching Brainiac as he fell into the mud. Brainiac was overwhelmed as he got up, surrounded by flies and microscopic bacteria.

"Brainy had found peace with all this. But you… Collector of Worlds… all you do, is drain from your space like a coward." Kara said.

Brainiac was overwhelmed as he attacked again but Kara dodged the punch and slammed Brainiac to the ground before he ended up with a glassy look. Kara considered as she pulled a punch, about to finish him off.

* * *

Lena, Vasquez and other agents and citizens of National City came to as they looked around in surprise. "What… what happened?"

* * *

Barry sped towards Kara as she unclenched her fist. "Is it over?"

"More or less. We need to reboot Brainy somehow." Kara said as Brainy was catatonic on the ground. She was surprised that she felt this fury inside of her. She was about to kill her friend.

**Notes for the Chapter:**

> The fight was a mix of comic books with Brainiac, Superman: Unbound animated film and a little reference to Smallville 8x11.
> 
> The next chapter will be a concluding epilogue to this story, since I wasn't planning for this story to be long.
> 
> So, what do you guys think?
> 
> Please review and let me know if you have enjoyed this and want for me to continue.


	9. Epilogue

**Summary for the Chapter:**

> Everyone deals with the aftermath of Brainiac's attack.

**Notes for the Chapter:**

> Disclaimer: I do not own DC Comics or the CW TV shows Arrow, The Flash, Legends of Tomorrow, Supergirl or any other characters or elements pertaining to the mentioned franchises.

Mon-El and Imra had been summoned from the future to help Brainy as the put him into the Legion ship and fixed him.

And then… the day of reckoning came.

* * *

"We all know that the world changes every day. And sometimes… people can become compromised by what comes from across the stars, just like Supergirl. What happened to Agent Dox isn't any different." J'onn said. "What happened after the Coluan ship, that wasn't Brainy. And he is still a valuable asset to the DEO. And we need him."

The tribunal stared and considered before Colonel Haley spoke up. "Thank you, Mr. J'onzz for your input but this council had already come to the same conclusion as you. We see no need for punishment at this juncture."

Brainy stared in disbelief. "Are you serious?"

"What happened with Alexandra Danvers, is a great tragedy and she was a valuable asset to this country and DEO. Many of the people considered her family and friends." Colonel Haley said, as Kara looked down briefly. "She knew the risks and accepted them. Her death was a tragic, yet inevitable casualty in the mission of DEO. You will undergo thorough checks to be sure that you are not compromised, Agent Dox and if you are clear, we shall reinstate you as soon as possible."

"I killed her!" Brainy snapped.

"Did he? Would Querl Dox in sound state of mind willingly kill Miss Danvers? Anyone, if you were not taken over by Brainiac?" Colonel Haley pointed out.

"No." Brainy admitted. "But that does not change the fact that she died by my hand."

Colonel Haley looked at him in sympathy. "And you will have to live with it for the rest of your days. I'm afraid that sentence is far more severe than any this council could mete out, Mr. Dox. I'm truly sorry."

Brainy looked down, as if he was not recognizing himself anymore.

"This meeting is adjourned." Colonel Haley said as she and the councilmen left.

* * *

**_DEO_ **

"I killed her." Brainy stared as he sat down.

"That wasn't you, Brainy." Oliver assured him.

"How am I supposed to live with it?" Brainy asked.

"You need to find a way to forgive yourself. Otherwise it's going to eat you up forever." Oliver held his shoulder.

"What if I can't?" Brainy wondered, unsure of himself.

"Ask yourself, 'What would Alex want?'. She'd want you to continue fight for what she had been fighting for. Keep going on. That's the least you owe her." Oliver said as Brainy considered.

* * *

_**National City Cemetery** _

"Alex fought for all of us every day. She fought for safety of both humans and aliens on this planet. She was a good person." Kara said. "And we will remember her that way."

Eliza, Lena, James, Kelly, Nia, Winn and others, doctors and DEO agents were at the funeral, mourning. Brainy didn't feel like if he should come, as much as everyone understood and forgave him.

* * *

Barry and Kara walked down the cemetery.

"Are you gonna be OK?" Barry asked.

"I was gonna kill Brainy. I was tempted to do it." Kara said.

Barry nodded. "I know how you feel. When Zoom killed my Dad, I almost was going to kill him. But I couldn't bring myself to. I didn't want to give him the satisfaction of being right. I thought he was my friend and mentor but again, I was fooled."

"This is… does the pain ever go away?" Kara wondered.

"I don't know. Sometimes it's gonna feel like a lifetime ago." Barry said. "Sometimes, it's gonna feel like yesterday."

"I feel like there's a hole inside me without her." Kara tapped her chest.

"Kara, if you need anything…"

Kara nodded as she hugged Barry tightly.

"Goodbye, Barry."

"Goodbye, Kara."

* * *

Brainy was alone in a bar before Nia and J'onn sat next to him. "Brainy... you need to find a way to make peace with it."

"How?" Brainy questioned.

"Come on, I think you and Nia can help me in my office. If you want to help people... Detective Dox." J'onn offered and Brainy considered.

"I think it can be fun." Nia smiled.

* * *

_**L-Corp** _

"Looks like the serum stopped working." Lena said as she examined the Harun-El serum and James's physical condition.

"Lena, I think we should stop this project." James said. "I felt… different and angry…"

"James, this can help humanity, I know it—"

"At what cost? You've seen what happened. Let it go." James said. "After what happened with Lockwood, the government and the Elite, do you still trust the government?"

Lena considered.

"I'm not saying I won't support you. But we need to think about this." James said.

"You're right." Lena said, deciding to let the project go.

* * *

_**National City** _

Two muggers were harassing a woman before one of them pulled out a gun. Supergirl threw him away, sending him crashing towards a wall.

"Have you lost your mind?" One of the muggers demanded. "Are you on something again?"

"No. I'm gonna make sure you can't hurt anyone again." Kara sneered, breaking his arm, full of grief and anger.

**Notes for the Chapter:**

> Not sure of this story, since I wasn't planning on making it long.
> 
> I honestly am surprised Lena would trust the government and share with them her research of Harun-El. If she wanted to just help humanity by curing diseases etc., fine but it's run by people with agenda and agendas can change and one would expect her to have trust issues after how Kara used James to spy on her in Season 3 but I do understand both her and James' point of view.
> 
> Plus, as much as Lena's intentions with Harun-El were genuine, she couldn't have been so naive to trust the government, if one considers what Ben Lockwood and Eve did with the Harun-El serum. I just don't think that Lena would be that naive, mainly after how Kara went behind her back. Eve being traitor and Lex's spy all along from the very start was a neat twist but it just didn't work for this story.
> 
> I think we can all agree that Kara's ego and self-righteousness in Season 3 was annoying but if I recall, she displayed almost no signs of it in Seasons 4-5. And Dark Kara is always interesting and with good writing and a really great tragedy, I can easily see her go off the deep end.
> 
> Please review and let me know if you have enjoyed the story to its end.
> 
> With regards
> 
> Bl4ckHunter


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